Re: [Freesurfer] MPRAGE SNR
Dear John FS's QA tools provide the SNR see https://surfer.nmr.mgh.harvard.edu/fswiki/QATools there is also a FS function called wm-anat-snr that can be used for that. Hope this helps Cheers Jürgen - Jürgen Hänggi, Ph.D. Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haen...@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. - Am 18.10.2015 um 16:48 schrieb John Anderson: > Dear Experts, > Is there any tool in Freesurfer that can help to evaluate the SNR for T1 > MPRAGE images directly ( i.e script). If not knidly can any help me to figure > out the best way to dao it. > > I highly appreciate your help! > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
It works pretty well, thanks ! > On Oct 18, 2015, at 14:10, Bruce Fischl wrote: > > you can use the -cm flag, but you might want to try out a beta of v6 instead > of 5.3 > On Sun, 18 Oct 2015, Yun Wang wrote: > >> Glad to hear this ! So how should I specify high resolution structure using >> recon-all command? >> >> >>> On Oct 17, 2015, at 10:09, Bruce Fischl wrote: >>> >>> High resolution fMRI has always been supported. V6 beta has better support >>> for high-resolution structurals. If your fMRI is higher than 1mm isotropic >>> then having higher res structurals (and hence denser cortical meshes) might >>> be useful >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Sat, 17 Oct 2015, Yun Wang wrote: >>> Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it? On Jun 25, 2015, at 13:36, Allison Moreau wrote: Hi Falk and Thomas, We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. -Allison On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: Hi Thomas, this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data. Best, Falk P.S. Following your instructions one will definitely become a coffee junkie. :D Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) Gesendet: Mittwoch, 24. Juni 2015 14:35 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data Hello! I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments! Best, Thomas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
you can use the -cm flag, but you might want to try out a beta of v6 instead of 5.3 On Sun, 18 Oct 2015, Yun Wang wrote: Glad to hear this ! So how should I specify high resolution structure using recon-all command? On Oct 17, 2015, at 10:09, Bruce Fischl wrote: High resolution fMRI has always been supported. V6 beta has better support for high-resolution structurals. If your fMRI is higher than 1mm isotropic then having higher res structurals (and hence denser cortical meshes) might be useful cheers Bruce On Sat, 17 Oct 2015, Yun Wang wrote: Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it? On Jun 25, 2015, at 13:36, Allison Moreau wrote: Hi Falk and Thomas, We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. -Allison On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: Hi Thomas, this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data. Best, Falk P.S. Following your instructions one will definitely become a coffee junkie. :D Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) Gesendet: Mittwoch, 24. Juni 2015 14:35 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data Hello! I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments! Best, Thomas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
Glad to hear this ! So how should I specify high resolution structure using recon-all command? > On Oct 17, 2015, at 10:09, Bruce Fischl wrote: > > High resolution fMRI has always been supported. V6 beta has better support > for high-resolution structurals. If your fMRI is higher than 1mm isotropic > then having higher res structurals (and hence denser cortical meshes) might > be useful > > cheers > Bruce > > > > On Sat, 17 Oct 2015, Yun Wang wrote: > >> Can the recon-all for high resolution fMRI data be used in V6 beta >> freesurfer now? If >> so, how to use it? >> >> On Jun 25, 2015, at 13:36, Allison Moreau >> wrote: >> Hi Falk and Thomas, >> We are actually working on testing the -hires flag now for the v6 release. We >> intend to release it with v6. >> -Allison >> On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: >> Hi Thomas, >> >> this looks like a really nice script and a lot better than my own. In the >> upcoming release of FreeSurfer v.6 my work-around probably is not needed >> anymore. However, I haven’t been able to have a look at the dev release yet >> and whether the standard recon-all features a flag to process high >> resolution data. >> >> Best, >> Falk >> >> P.S. Following your instructions one will definitely become a coffee >> junkie. :D >> >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard >> .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) >> Gesendet: Mittwoch, 24. Juni 2015 14:35 >> An: freesurfer@nmr.mgh.harvard.edu >> Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data >> >> Hello! >> >> I wrote a bash script some time ago to process data acquired at a >> sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink >> (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might >> be helpful for others, too, as there are some questions about it in the >> mailing list archives, so here it >> is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy >> about any comments! >> >> Best, >> Thomas >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MPRAGE SNR
Dear Experts, Is there any tool in Freesurfer that can help to evaluate the SNR for T1 MPRAGE images directly ( i.e script). If not knidly can any help me to figure out the best way to dao it. I highly appreciate your help! Bests, John Anderson Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
